The coherent control of quantum states has been a subject of research for as long as quantum systems have been artificially created in laboratories. The prospect of one day realizing a quantum computer, relying on the coherence properties of quantum systems to multiply the available computational power, is of course one important motivation in that direction. It is not the only one. A precise control allows to initialize systems in specific quantum states and manipulate them in order e.g. to realize precision measurements. Ultracold atoms are an ideal test bed for advanced control schemes. Their isolation from the environment gives them long coherence times, while their response to external excitations is relatively simple to probe compared to other systems. Moreover, they offer a wide tuning range for a variety of parameters, such as density or interaction strength, and thus the possibility to experimentally investigate a whole spectrum of quantum theories. Coherent control of quantum states in ultracold atomic systems is therefore a rich area of research, holding promises both for fundamental tests of quantum mechanics and practical applications. In this thesis, we developed a scheme to coherently manipulate the motional states of a Bose-Einstein condensate, in a way that is not only preserving the coherence of the system, but is also fast compared to the typical timescales of the system. The experimental system is an elongated condensate on an atomchip, initially in its transverse ground state. The condensate is displaced transversely to excite higher motional states. Using optimal control theory, the displacement is optimized to target specific motional states or a superposition of them. The optimizations rely on a mean-field approximation of the condensate. Both theoretically and experimentally, specific motional state superpositions could be reached in 1.1 ms with efficiencies higher than 98 %. This control method was applied to the demonstration of a motional state interferometer. In this interferometer, the two paths are the ground and first transverse excited states, while a phase is naturally accumulated in the time between two optimized displacement pulses acting as beam splitters. In this scheme, the challenge lies in the optimization of a pulse that is effective for all phases. The interferometer was optimized numerically and successfully implemented experimentally, yielding an initial contrast of 92 %. The created motional state superpositions are not stable and a damping is observed on a timescale of about 10 ms. To gain insight into the physics of the system, several damping mechanisms are envisaged and models developed. In particular, the dephasing and decoherence phenomena taking place in the longitudinal direction of the condensate are investigated. A transverse many-body model including three motional state is also designed. Timescales of the damping and dependencies on parameters such as atom number and temperature are extracted and compared to experimental data. From this study, interesting elements on the physics of the motional state superpositions came to light. The results presented in this thesis demonstrate fast and efficient control over motional states and pave the way toward practical applications, such as a motional state interferometer. They also open a new direction for fundamental questions on out-of-equilibrium physics in closed systems.